title: Plastome sequences of Lygodium japonicum and Marsilea crenata reveal the genome organization transformation from basal ferns to core leptosporangiates.
abstract: Previous studies have shown that core leptosporangiates, the most species-rich group of extant ferns (monilophytes), have a distinct plastid genome (plastome) organization pattern from basal fern lineages. However, the details of genome structure transformation from ancestral ferns to core leptosporangiates remain unclear because of limited plastome data available. Here, we have determined the complete chloroplast genome sequences of Lygodium japonicum (Lygodiaceae), a member of schizaeoid ferns (Schizaeales), and Marsilea crenata (Marsileaceae), a representative of heterosporous ferns (Salviniales). The two species represent the sister and the basal lineages of core leptosporangiates, respectively, for which the plastome sequences are currently unavailable. Comparative genomic analysis of all sequenced fern plastomes reveals that the gene order of L. japonicum plastome occupies an intermediate position between that of basal ferns and core leptosporangiates. The two exons of the fern ndhB gene have a unique pattern of intragenic copy number variances. Specifically, the substitution rate heterogeneity between the two exons is congruent with their copy number changes, confirming the constraint role that inverted repeats may play on the substitution rate of chloroplast gene sequences.
authors.affiliation: CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Gao
authors.forename: Bo
authors.initials: B
authors.lastname: Wang
authors.forename: Zhi-Wei
authors.initials: ZW
authors.lastname: Wang
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zhou
authors.forename: Ying-Juan
authors.initials: YJ
authors.lastname: Su
authors.forename: Ting
authors.initials: T
authors.lastname: Wang
mesh_terms: D056915:DNA Copy Number Variations; D019143:Evolution, Molecular; D029624:Ferns / Q000235:genetics*; D023061:Gene Order; D017343:Genes, Plant; D054628:Genome, Chloroplast; D055029:Inverted Repeat Sequences; D043964:Marsileaceae / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D010940:Plant Proteins
keywords: chloroplast genome; core leptosporangiates; heterosporous ferns; intragenic rate heterogeneity; ndhB; schizaeoid ferns